Compositions inducing cleavage of RNA motifs

ABSTRACT

Disclosed are compositions inducing cleavage of an RNA substrate, as well as their use for inducing cleavage of RNA substrates in vitro and in vivo. The compositions contain part of an active center, with the other part of the active center provided by the RNA substrate. The subunits of the active center region of the compositions are nucleotides and/or nucleotide analogues. The disclosed compositions also have flanking regions contributing to the formation of a specific hybridization with an RNA substrate. Preferred compositions form, in combination with an RNA substrate, a structure resembling a hammerhead structure. The active center of the disclosed compositions is characterized by the presence of I 15.1  which allows cleavage of RNA substrates having C 16.1 .

BACKGROUND OF THE INVENTION

[0001] The present invention is in the field of compositions having RNA-cleavage activity.

[0002] Hammerhead ribozymes are an example of catalytic RNA molecules which are able to recognize and cleave a given specific RNA substrate (Hotchins et al., Nucleic Acids Res. 14:3627 (1986); Keese and Symons, in Viroids and viroid—like pathogens (J. J. Semanchik, publ., CRC-Press, Boca Raton, Fla., 1987), pages 147). The catalytic center of hammerhead ribozymes is flanked by three stems and can be formed by adjacent sequence regions of the RNA or also by regions which are separated from one another by many nucleotides. FIG. 1 shows a diagram of such a catalytically active hammerhead structure. The stems have been denoted I, II and III. The nucleotides are numbered according to the standard nomenclature for hammerhead ribozymes (Hertel et al., Nucleic Acids Res. 20:3252 (1992)). In this nomenclature, bases are denoted by a number which relates their position relative to the 5′ side of the cleavage site. Furthermore, each base that is involved in a stem or loop region has an additional designation (which is denoted by a decimal point and then another number) that defines the position of that base within the stem or loop. A designation of N^(11.3) would indicate that this base is involved in a paired region and that it is the third base in that stem going away for the core region. This accepted convention for describing hammerhead derived ribozymes allows for the nucleotides involved in the core of the enzyme to always have the same number relative to all of the other nucleotides. The size of the stems involved in substrate binding or core formation can be any size and of any sequence, and the position of A⁹, for example, will remain the same relative to all of the other core nucleotides. Nucleotides designated, for example, N^ ¹² or N⁹^ represent an inserted nucleotide where the position of the carrot (^ ) relative to the number denotes whether the insertion is before or after the indicated nucleotide. Thus, N^ ¹² represents a nucleotide inserted before nucleotide position 12, and N^ ⁹ represent a nucleotide inserted after nucleotide position 9.

[0003] The consensus sequence of the catalytic core structure is described by Ruffner and Uhlenbeck (Nucleic Acids Res. 18:6025-6029 (1990)). Perriman et al. (Gene 113:157-163 (1992)) have meanwhile shown that this structure can also contain variations, for example, naturally occurring nucleotide insertions such as N⁹^ and N^ ¹². Thus, the positive strand of the satellite RNA of the tobacco ring-spot virus does not contain any of the two nucleotide insertions while the +RNA strand of the virusoid of the lucerne transient streak virus (vLTSV) contains a N⁹^ =U insertion which can be mutated to C or G without loss of activity (Sheldon and Symons, Nucleic Acids Res. 17:5679-5685 (1989)). Furthermore, in this special case, N⁷=A and R^(15.1)=A. On the other hand, the minus strand of the carnation stunt associated viroid (−CarSV) is quite unusual since it contains both nucleotide insertions, that is N^ ¹²=A and N⁹^ =C (Hernandez et al., Nucleic Acids Res. 20:6323-6329 (1992)). In this viroid N⁷ =A and R^(15.1)=A. In addition, this special hammerhead structure exhibits a very effective self-catalytic cleavage despite the more open central stem.

[0004] Possible uses of hammerhead ribozymes include, for example, generation of RNA restriction enzymes and the specific inactivation of the expression of genes in, for example, animal, human or plant cells and prokaryotes, yeasts and plasmodia. A particular biomedical interest is based on the fact that many diseases, including many forms of tumors, are related to the overexpression of specific genes. Inactivating such genes by cleaving the associated mRNA represents a possible way to control and eventually treat such diseases. Moreover there is a great need to develop antiviral, antibacterial and antifungal pharmaceutical agents. Ribozymes have potential as such anti-infective agents since viral expression can be blocked selectively by cleaving viral or microbial RNA molecules vital to the survival of the organism can be selectively destroyed.

[0005] In addition to needing the correct hybridizing sequences for substrate binding, substrates for hammerhead ribozymes have been shown to strongly prefer the triplet N^(16.2)U^(16.1)H¹⁷ where N can be any nucleotide, U is uridine, and H is either adenosine, cytidine, or uridine (Koizumi et al., FEBS Lett. 228, 228-230 (1988); Ruffner et al., Biochemistry 29, 10695-10702 (1990); Perriman et al., Gene 113, 157-163 (1992)). The fact that changes to this general rule for substrate specificity result in non-functional substrates implies that there are “non core compatible” structures which are formed when substrates are provided which deviate from the stated requirements. Evidence along these lines was recently reported by Uhlenbeck and co-workers (Biochemistry 36:1108-1114 (1997)) when they demonstrated that the substitution of a G at position 17 caused a functionally catastrophic base pair between G¹⁷ and C³ to form, both preventing the correct orientation of the scissile bond for cleavage and the needed tertiary interactions of C³ (Murray et al., Biochem. J. 311:487494 (1995)). The strong preference for a U at position 16.1 may exist for similar reasons. Many experiments have been done in an attempt to isolate ribozymes which are able to efficiently relieve the requirement of a U at position 16.1, however, attempts to find hammerhead type ribozymes which can cleave substrates having a base other than a U at position 16.1 have proven impossible (Perriman et al., Gene 113,

[0006] Efficient catalytic molecules with reduced or altered requirements in the cleavage region are highly desirable because their isolation would greatly increase the number of available target sequences that molecules of this type could cleave. For example, it would be desirable to have a ribozyme variant that could efficiently cleave substrates containing triplets other than N^(16.2)U¹⁶¹H¹⁷ since this would increase the number of potential target cleavage sites.

[0007] Chemically modified oligonucleotides which contain a block of deoxyribonucleotides in the middle region of the molecule have potential as pharmaceutical agents for the specific inactivation of the expression of genes (Giles et al., Nucleic Acids Res. 20:763-770 (1992)). These oligonucleotides can form a hybrid DNA-RNA duplex in which the DNA bound RNA strand is degraded by RNase H. Such oligonucleotides are considered to promote cleavage of the RNA and so cannot be characterized as having an RNA-cleaving activity nor as cleaving an RNA molecule (the RNase H is cleaving). A significant disadvantage of these oligonucleotides for in vivo applications is their low specificity, since hybrid formation, and thus cleavage, can also take place at undesired positions on the RNA molecules.

[0008] Previous attempts to recombinantly express catalytically active RNA molecules in the cell by transfecting the cell with an appropriate gene have not proven to be very effective since a very high expression was necessary to inactivate specific RNA substrates. In addition the vector systems which are available now cannot generally be applied. Furthermore, unmodified ribozymes cannot be administered directly due to the sensitivity of RNA to degradation by RNases and their interactions with proteins. Thus, chemically modified active substances have to be used in order to administer hammerhead ribozymes exogenously (discussed, for example, by Heidenreich et al., J. Biol. Chem. 269:2131-2138 (1994); Kiehntopf et al., EMBO J. 13:4645-4652 (1994); Paolella et al., EMBO J. 11: 1913-1919 (1992); and Usman et al., Nucleic Acids Symp. Ser. 31:163-164 (1994)).

[0009] U.S. Pat. No. 5,334,711 describes such chemically modified active substances based on synthetic catalytic oligonucleotide structures with a length of 35 to 40 nucleotides which are suitable for cleaving a nucleic acid target sequence and contain modified nucleotides that contain an optionally substituted alkyl, alkenyl or alkynyl group with 1-10 carbon atoms at the 2′-O atom of the ribose. These oligonucleotides contain modified nucleotide building blocks and form a structure resembling a hammerhead structure. These oligonucleotides are able to cleave specific RNA substrates. Examples of oligonucleotides are described having an active center which has a length of 14 nucleotides and which contains several ribonucleotides. These ribonucleotides increase the sensitivity of the oligonucleotide to enzymes which cleave RNA. A further disadvantage is the length of the active center which can often lead to unspecific hybridization.

[0010] WO 95/11304 describes RNA-cleaving nucleic acids with an active center that is free of ribonucleotide building blocks but instead contains deoxyribonucleotides. However, the deoxyribonucleotides used in the active center result in a very low RNA cleavage activity. Thus, it was reported that a 13-mer deoxyribozyme of the “GAAA” type based on LTSV was not able to cleave a 41-mer oligoribonucleotide substrate while the corresponding 13-mer ribozyme exhibited catalytic activity (Jeffries and Symons, Nucleic Acids Res. 17:1371-1377 (1989)).

[0011] WO 97/18312 describes oligomers which contain only part of a catalytic core resembling a hammerhead catalytic core. These oligomers, when associated with an RNA substrate having a motif resembling the complementary part of a catalytic core, induce cleavage of the RNA substrate. The RNA substrates for use with these oligomers all have a U at position 16.1.

[0012] The use of a large number of deoxyribonucleotides in the hybridization arms or in the active center can lead to a loss of specificity due to an activation of RNase H since sequences which are related to the desired target sequence can also be cleaved. Moreover, catalytic DNA oligomers are not particularly well suited for in vivo applications due to interactions with proteins, and lack of resistance to degradation by nucleases.

[0013] The shortest ribozymes that have been previously used have a minimum length of 15+N+M nucleotides, the active center being 15 nucleotides long and N and M being the length of the recognition sequences (Benseler et al., J. Am. Chem. Soc. 115:8483-8484 (1993)). Such ribozymes also contain ribonucleotides in at least five positions of the catalytic center (Paolella et al., EMBO J. 11:1913-1919 (1992), and Yang et al., Bio-chemistry 31:5005-5009 (1992)).

[0014] It is therefore an object of the present invention to provide compositions that induce cleavage of RNA, and in particular to provide oligomers that induce cleavage of RNA and which at the same time have a high stability, activity, and specificity.

[0015] It is another object of the present invention to provide compositions that induce cleavage of RNA substrates having a cleavage site triplet other than N^(16.2)U^(16.1)H¹⁷.

SUMMARY OF THE INVENTION

[0016] Disclosed are compositions inducing cleavage of an RNA substrate, as well as their use for inducing cleavage of RNA substrates in vitro and in vivo. The compositions contain part of an active center, with the other part of the active center provided by the RNA substrate. The subunits of the active center region of the compositions are nucleotides and/or nucleotide analogues. The disclosed compositions also have flanking regions contributing to the formation of a specific hybridization with an RNA substrate. Preferred compositions form, in combination with an RNA substrate, a structure resembling a hammerhead structure. The active center of the disclosed compositions is characterized by the presence of I^(15.1) which allows cleavage of RNA substrates having C^(16.1).

BRIEF DESCRIPTION OF THE DRAWINGS

[0017]FIG. 1 is a diagram of a hammerhead structure and the, corresponding nomenclature (SEQ ID NO:1). Cleavage occurs between H¹⁷ and N^(1.1) to generate the 2′-3′-cyclic phosphate at H ¹⁷.

[0018]FIG. 2 is a diagram of an RNA substrate (SEQ ID NO:3) in association with an example of an oligomer (SEQ ID NO:2) that induces cleavage of the RNA substrate. The structure formed by the oligomer and the substrate resembles the structure of a hammerhead ribozyme, with each providing a part of the elements corresponding to the catalytic core. In this case, the substrate makes up half of stems II and III and all of stem I, and loops II and III are not present. Cleavage occurs 3′ of HI¹⁷.

[0019]FIG. 3 is a diagram showing the interaction of the A^(15.1)-U^(16.1) base pair in hammerhead ribozymes (top), and the predicted isostructural interaction of a I^(15.1)-C^(16.1) base pair (bottom) that replaces the A^(15.1) -U^(16.1) base pair.

DETAILED DESCRIPTION OF THE INVENTION

[0020] Disclosed are compositions inducing cleavage of an RNA substrate, as well as their use for inducing cleavage of RNA substrates in vitro and in vivo. The compositions contain part of an active center, with the other part of the active center provided by the RNA substrate. The subunits of the active center region of the compositions are nucleotides and/or nucleotide analogues. The disclosed compositions also have flanking regions contributing to the formation of a specific hybridization with an RNA substrate. Preferred compositions form, in combination with an RNA substrate, a structure resembling a hammerhead structure. The active center of the disclosed compositions is characterized by the presence of I15.1 which allows cleavage of RNA substrates having C^(16.1).

[0021] All naturally occurring hammerhead ribozymes have an A^(15.1)-U^(16.1) base pair. In addition, it is known that substrates for ribozymes based on the consensus hammerhead sequence strongly prefer a substrate that contains an N^(16.2)U^(16.1)H¹⁷ triplet in which H¹⁷ is not a guanosine (Koizumi et al., FEBS Lett. 228, 228-230 (1988); Ruffner et al., Biochemistry 29, 10695-10702 (1990); Perriman et al., Gene 113, 157-163 (1992)). Many experiments have been done in an attempt to isolate ribozymes which are able to efficiently relieve the requirement of a U at position 16.1, however, attempts to find ribozymes which can cleave substrates having a base other than a U at position 16.1 have proven impossible (Perriman et al., Gene 113, 157-163 1992, Singh et al., Antisense and Nucleic Acid Drug Development 6:165-168 (1996)).

[0022] However, examination of the recently published X-ray crystal structures (Pley et al., Nature 372:68-74 (1994), Scott et al., Cell 81:991-1002 (1995), and Scott et al., Science 274:2065-2069 (1996)) led to the realization that the A^(15.1)-U^(16.1) interaction is a non-standard base pair with a single hydrogen bond between the exocyclic amine (N6) of the adenosine and the 4-oxo group of the uridine. Modeling studies (based on the crystal structure) then led to the discovery that the interaction of the wild-type A^(15.1)-U^(16.1) base pair can be spatially mimicked by replacement with an I^(15.1)-C^(16.1) base pair that adopts an isostructural orientation and which preserves the required contact of the 2-keto group of C^(16.1) with A⁶ of the uridine turn. In the model, the polarity of the stabilizing hydrogen bond between positions 15.1 and 16.1 is reversed in the I^(15.1)-C^(16.1) interaction, but the correct orientation of the bases around this bond is maintained.

[0023] It has been discovered that Gerlach type ribozyme analogues containing an inosine at position 15.1 readily cleave RNA substrates containing an N^(16.2)C^(16.1)H¹⁷ triplet. Based on this, disclosed are compositions, preferably synthetic oligomers, which induce cleavage of a nucleic acid target sequence containing the structure 5′-Z₃′-C^(16.1)-X¹⁷-S-Z₄-Z₁′-3′ where S is capable of forming a stem and loop and Z₄ corresponds to part of an active center. It is preferred that X¹⁷ is not guanosine. The ability to induce cleavage of substrates having N^(16.1)C^(16.1)X¹⁷ triplets effectively doubles the number of targets available for cleavage using compositions of the type disclosed.

Compositions Inducing RNA Cleavage in a Substrate

[0024] Specifically disclosed is a composition that induces cleavage of an RNA substrate, where the composition includes a structure 5′-Z₁-Z₂-Z₃-3′. Elements Z₁ and Z₃ are each oligomeric sequences which are made up of nucleotides, nucleotide analogues, or a combination of both, or are oligonucleotide analogues. The oligomeric sequences of elements Z₁ and Z₃ specifically interact with the RNA substrate, preferably by hybridization.

[0025] In these preferred compositions, element Z₂ has a structure of

5′-X¹²X¹³X¹⁴X^(15.1)-3′, or

5-X^ ¹²X¹²X¹³X¹⁴X^(15.1)-3′.

[0026] Element Z₂ in these preferred compositions is made up of nucleotides, nucleotide analogues, or a combination of both. The nucleotides and nucleotide analogues in element Z₂ each have the structure

[0027] In structure (I) each B can be adenin-9-yl, cytosin-1-yl, guanin-9-yl, uracil-1-yl, uracil-5-yl, hypoxanthin-9-yl, thymin-1-yl, 5-methylcytosin-1-yl, 2,6-diaminopurin-9-yl, purin-9-yl, 7-deazaadenin-9-yl, 7-deazaguanin-9-yl, 5-propynylcytosin-1-yl, 5-propynyluracil-1-yl, isoguanin-9-yl, 2-aminopurin-9-yl, 6-methyluracil-1-yl, 4-thiouracil-1-yl, 2-pyrimidone-1-yl, quinazoline-2,4-dione-1-yl, xanthin-9-yl, N²-dimethylguanin-9-yl or a functional equivalent thereof;

[0028] Each V can be an O, S, NH, or CH₂ group.

[0029] Each W can be —H, —OH, —COOH, —CONH₂, —CONHR¹, —CONR¹R², —NH₂, —NHR¹, —NR¹R², —NHCOR¹, —SH, SR¹, —F, —ONH₂, —NHR¹, —ONR¹R², —NHOH, —NHOR¹, —NR²OH, —NR²OR¹, substituted or unsubstituted C₁-C₁₀ straight chain or branched alkyl, substituted or unsubstituted C₂-C₁₀ straight chain or branched alkenyl, substituted or unsubstituted C₂-C₁₀ straight chain or branched alkynyl, substituted or unsubstituted C₁-C₁₀ straight chain or branched alkoxy, substituted or unsubstituted C₂-C₁₀ straight chain or branched alkenyloxy, and substituted or unsubstituted C₂-C₁₀ straight chain or branched alkynyloxy. The substituents for W groups are independently halogen, cyano, amino, carboxy, ester, ether, carboxamide, hydroxy, or mercapto. R¹ and R² can be substituted or unsubstituted alkyl, alkenyl, or alkynyl groups, where the substituents are independently halogen, cyano, amino, carboxy, ester, ether, carboxamide, hydroxy, or mercapto.

[0030] D and E are residues which together form a phosphodiester or phosphorothioate diester bond between adjacent nucleosides or nucleoside analogues or together form an analogue of an internucleosidic bond.

[0031] B is hypoxanthin-9-yl, or a functional equivalent thereof, in X^(15.1); B can be guanin-9-yl, hypoxanthin-9-yl or 7-deazaguanin-9-yl in X¹²; B can be adenin-9-yl, 2,6-diaminopurin-9-yl, purin-9-yl or 7-deazaadenin-9-yl in X¹³ and X¹⁴; and B can be adenin-9-yl, cytosin-1-yl, guanin-9-yl, uracil-1-yl, uracil-5-yl, hypoxanthin-9-yl, thymin-1-yl, 5-methylcytosin-1-yl, 2,6-diaminopurin-9-yl, purin-9-yl, 7-deazaadenin-9-yl, 7-deazaguanin-9-yl, 5-propynylcytosin-1-yl, 5-propynyluracil-1-yl, isoguanin-9-yl, 2-aminopurin-9-yl, 6-methyluracil-1-yl, 4-thiouracil-1-yl, 2-pyrimidone-1-yl, quinazoline-2,4-dione-1-yl, xanthin-9-yl, N²-dimethylguanin-9-yl or a functional equivalent thereof in X^ ¹². B of X^(15.1) is preferably an analog of hypoxanthin-9-yl, preferably where no hydrogen bond can form between any group at the 2 position of the base and the 2-oxo group of C^(16.1). Preferably, B is not guanin-9-yl in X^(15.1).

[0032] B in X¹², X¹³, and X¹⁴ can also be a functionally equivalent nucleobase within the context of the catalytic core of a hammerhead ribozyme.

[0033] The disclosed compositions have significant advantages. For example, the disclosed compositions require only 4+N+M or 5+N+M monomeric units (for example, nucleotides) in which N and M are preferably numbers in the range of 5 to 10. Furthermore, the disclosed compositions can contain a significantly smaller number of natural ribonucleotides without loss of activity. Due to the reduced length and reduced number of ribonucleotides, the disclosed compositions are more conveniently and easily synthesized, and can be more stable in vivo, than Gerlach type ribozymes. The in vivo stability can be increased by a further reduction in the number of ribonucleotides.

Definitions

[0034] As used herein, oligomer refers to oligomeric molecules composed of subunits where the subunits can be of the same class (such as nucleotides) or a mixture of classes. It is preferred that the disclosed oligomers be oligomeric sequences. It is more preferred that the disclosed oligomers be oligomeric sequences. Oligomeric sequences are oligomeric molecules where each of the subunits includes a nucleobase (that is, the base portion of a nucleotide or nucleotide analogue) which can interact with other oligomeric sequences in a base-specific manner. The hybridization of nucleic acid strands is a preferred example of such base-specific interactions. Oligomeric sequences preferably are comprised of nucleotides, nucleotide analogues, or both, or are oligonucleotide analogues.

[0035] As used herein, nucleoside refers to adenosine, guanosine, cytidine, uridine, 2′-deoxyadenosine, 2′-deoxyguanosine, 2′-deoxycytidine, or thymidine. A nucleoside analogue is a chemically modified form of nucleoside containing a chemical modification at any position on the base or sugar portion of the nucleoside. As used herein, the term nucleoside analogue encompasses, for example, both nucleoside analogues based on naturally occurring modified nucleosides, such as inosine and pseudouridine, and nucleoside analogues having other modifications, such as modifications at the 2′ position of the sugar. As used herein, nucleotide refers to a phosphate derivative of nucleosides as described above, and a nucleotide analogue is a phosphate derivative of nucleoside analogues as described above. The subunits of oligonucleotide analogues, such as peptide nucleic acids, are also considered to be nucleotide analogues.

[0036] As used herein, a ribonucleotide is a nucleotide having a 2′ hydroxyl function. Analogously, a 2′-deoxyribonucleotide is a nucleotide having only 2′ hydrogens. Thus, ribonucleotides and deoxyribonucleotides as used herein refer to naturally occurring nucleotides having nucleoside components adenosine, guanosine, cytidine, and uridine, or 2′-deoxyadenosine, 2′-deoxyguanosine, 2′-deoxycytidine, and thymidine, respectively, without any chemical modification. Ribonucleosides, deoxyribonucleosides, ribonucleoside analogues and deoxyribonucleoside analogues are similarly defined except that they lack the phosphate group, or an analogue of the phosphate group, found in nucleotides and nucleotide analogues.

[0037] As used herein, oligonucleotide analogues are polymers of nucleic acid-like material with nucleic acid-like properties, such as sequence dependent hybridization, that contain at one or more positions, a modification away from a standard RNA or DNA nucleotide. A preferred example of an oligonucleotide analogue is peptide nucleic acid.

[0038] As used herein, base pair refers to a pair of nucleotides or nucleotide analogues which interact through one or more hydrogen bonds. The term base pair is not limited to interactions generally characterized as Watson-Crick base pairs, but includes non-canonical or sheared base pair interactions (Topal and Fresco, Nature 263:285 (1976); Lomant and Fresco, Prog. Nucl. Acid Res. Mol. Biol. 15:185 (1975)). Thus, nucleotides A^(15.1) and U^(16.1) form a base pair in hammerhead ribozymes (see FIG. 1) but the base pair is non-canonical (see FIG. 3).

[0039] The internucleosidic linkage between two nucleosides can be achieved by phosphodiester bonds or by modified phospho bonds such as by phosphorothioate groups or other bonds such as, for example, those described in U.S. Pat. No. 5,334,711.

Flanking Elements Z₁ and Z₃

[0040] The monomeric subunits of elements Z₁ and Z₃ which flank the active center (formed by element Z₂) are preferably nucleotides and/or nucleotide analogues. Elements Z₁ and Z₃ are designed so that they specifically interact, preferably by hybridization, with a given RNA substrate and, together with the element Z₂, form a structure (preferably a structure resembling part of a hammerhead ribozyme) which induces specific cleavage of the RNA substrate.

[0041] The subunits of elements Z₁ and Z₃ can, on the one hand, be ribonucleotides. However, it is preferred that the number of ribonucleotides be as small as possible since the presence of ribonucleotides reduces the in vivo stability of the oligomers. Elements Z₁ and Z₃ (and also the active center Z₂) preferably do not contain any ribonucleotides at the positions containing pyrimidine nucleobases. Such positions preferably contain nucleotide analogues.

[0042] The use of a large number of deoxyribonucleotides in elements Z₁ and Z₃ is also less preferred since undesired interactions with proteins can occur or an unintended RNase H-sensitive DNA-RNA hybrid could form. Thus, elements Z₁ and Z₃ each preferably contain (1) no ribonucleotides, and (2) no sequences of more than 3 consecutive deoxyribonucleotides.

[0043] The subunits of elements Z₁ and Z₃ are preferably nucleotides, nucleotide analogues, or a combination. Preferably, the nucleotides and nucleotide analogues in elements Z₁ and Z₃ each have the structure

[0044] In structure (I) each B can be adenin-9-yl, cytosin-1-yl, guanin-9-yl, uracil-1-yl, uracil-5-yl, hypoxanthin-9-yl, thymin-1-yl, 5-methylcytosin-1-yl, 2,6-diaminopurin-9-yl, purin-9-yl, 7-deazaadenin-9-yl, 7-deazaguanin-9-yl, 5-propynylcytosin-1-yl, 5-propynyluracil-1-yl, isoguanin-9-yl, 2-aminopurin-9-yl, 6-methyluracil-1-yl, 4-thiouracil-1-yl, 2-pyrimidone-1-yl, quinazoline-2,4-dione-1-yl, xanthin-9-yl, N2-dimethylguanin-9-yl or a functional equivalent thereof;

[0045] Each V can be an O, S, NH, or CH₂ group.

[0046] Each W can be —H, —OH, —COOH, —CONH₂, —CONHR¹, —CONR¹R², —NH₂, —NHR¹, —NR¹R², —NHCOR¹, —SH, SR¹, —F, —ONH₂, —ONHR¹, —ONR¹R², —NHOH, —NHOR¹, —NR²OH, —NR²OR¹, substituted or unsubstituted C₁-C₁₀ straight chain or branched alkyl, substituted or unsubstituted C₂-C₁₀ straight chain or branched alkenyl, substituted or unsubstituted C₂-C₁₀ straight chain or branched alkynyl, substituted or unsubstituted C₁-C₁₀ straight chain or branched alkoxy, substituted or unsubstituted C₂-C₁₀ straight chain or branched alkenyloxy, and substituted or unsubstituted C₂-C₁₀ straight chain or branched alkynyloxy. The substituents for W groups are independently halogen, cyano, amino, carboxy, ester, ether, carboxamide, hydroxy, or mercapto. R¹ and R² can be substituted or unsubstituted alkyl, alkenyl, or alkynyl groups, where the substituents are independently halogen, cyano, amino, carboxy, ester, ether, carboxamide, hydroxy, or mercapto.

[0047] D and E are residues which together form a phosphodiester or phosphorothioate diester bond between adjacent nucleosides or nucleotide analogues or together form an analogue of an internucleosidic bond.

[0048] For elements Z₁ and Z₃ having nucleotide and/or nucleotide analogues of structure (I), it is preferred that each W is substituted or unsubstituted C₁-C₁₀ straight chain or branched alkoxy, C₂-C₁₀ straight chain or branched alkenyloxy, or C₂-C₁₀ straight chain or branched alkynyloxy.

[0049] In addition, the flanking elements Z₁ and Z3 can also contain nucleotide analogues such as peptide nucleic acids (also referred to as peptidic nucleic acids; see for example Nielsen et al., Science 254:1497-1500 (1991), and Dueholm et al., J. Org. Chem. 59:5767-5773 (1994)). In this case the coupling of individual subunits can, for example, be achieved by acid amide bonds. Elements Z₁ and Z₃, when based on peptide nucleic acids, can be coupled to element Z₂, based on nucleotides or nucleotide analogues, using either suitable linkers (see, for example, Petersen et al., BioMed. Chem. Lett. 5:1119-1121 (1995)) or direct coupling (Bergmann et al., Tetrahedron Lett. 36:6823-6826 (1995)). Where elements Z₁ and Z3 contain a combination of nucleotides (and/or nucleotide analogues) and peptide nucleic acid, similar linkages can be used to couple the different parts.

[0050] The subunits of the flanking elements Z₁ and Z3 contain nucleobases or nucleobase analogues which can hybridize or interact with nucleobases that occur naturally in RNA molecules. The nucleobases are preferably selected from naturally occurring bases (that is, adenine, guanine, cytosine, thymine and uracil) as well as nucleobase analogues, such as 2,6-diaminopurine, hypoxanthine, 5-methylcytosine, pseudouracil, 5-propynyluracil, and 5-propynylcytosine, which enable a specific binding to the target RNA.

[0051] A strong and sequence-specific interaction (that is, a more stable hybrid between the RNA substrate and the oligomer) between the RNA substrate and elements Z₁ and Z₃ is preferred. For this purpose, it is preferred that the following nucleobase analogues be used in oligomeric sequences of elements Z₁ and Z3 in place of the standard nucleobases: 2,6-diaminopurine instead of adenine; thymine or 5-propynyluracil instead of uracil; and 5-methylcytosine or 5-propynylcytosine instead of cytosine. 2-Amino-2′-O-alkyladenosines are also preferred (Lamm et al., Nucleic Acids Res. 19:3193-3198 (1991)). Furthermore, aromatic systems can be linked to positions 4 and 5 of uracil to produce nucleobase analogues such as phenoxazine, which can improve the stability of the double-strand (Lin et al., J. Am. Chem. Soc. 117:3873-3874 (1995)).

[0052] Preferred RNA substrates for cleavage using the disclosed compositions have the structure

5′-Z₃′-C^(16.1)-X¹⁷-S-Z₄-Z₁′-3′,

[0053] where Z₁′ and Z₃′ interact with Z₁ and Z₃, respectively, where C^(16.1) is cytidine, and where X¹⁷ is adenosine, guanosine, cytidine, or uridine. S is an RNA sequence capable of forming a hairpin structure with a length of preferably from 6 to 60 and more preferably of from 6 to 20 bases. Cleavage occurs 3′ of X¹⁷. Preferably, X¹⁷ is adenosine, cytidine, or uridine, more preferably X¹⁷ is adenosine or cytidine, and most preferably X¹⁷ is adenosine. Preferably, X^(16.2) (that is, the 3′ nucleoside in element Z₃′) is adenosine or guanosine. The target sites in substrates which can be cleaved using the disclosed compositions are distinct from target sites for hammerhead ribozymes since hammerhead ribozymes require a uridine in position 16.1 of the substrate.

[0054] Element Z₄ of the substrate has the structure

5′-X³X⁴X⁵X⁶X⁷X⁸X⁹-3′, or

5′-X³X⁴X⁵X⁶X⁷X⁸X⁹X⁹^ -3′

[0055] where X⁵ and X⁸ are both guanosine, X⁶ and X⁹ are both adenosine, X⁴ is uridine, X³ is cytidine, and X⁷ and X⁹^ are adenosine, guanosine, cytidine, or uridine. The disclosed composition, in combination with an RNA substrate containing a structure of element Z₄, can form a structure resembling a hammerhead as shown in FIG. 2.

[0056] It is preferred that Z₁ interact with Z₁′ in such a way as to stabilize the interactions between Z₂ and Z₄. Although preferred, it is not required that element Z₁ be present in the disclosed compositions. In this case, it is preferred that element Z₁′ (in the substrate) include a G at the 5′ end (that is, at the junction of elements Z₄ and Z₁′). Taira and co-workers (Amontov and Taira, J. Am. Chem. Soc. 118:1624-1628 (1996)) have shown that the stacking energy gained from a guanosine juxtaposed to R⁹ of a hammerhead-like ribozyme stabilizes the formation of a catalytic structure. Thus, it is preferred that the 5′ nucleotide of Z₁′ is G.

[0057] The cleavage motif C^(16.1)-X¹⁷-S-Z₄ occurs only rarely (approximately one motif for every 5000 to 10,000 nucleotides). This, taken together with the individually selected recognition sequences, means that, statistically, a composition as disclosed should induce cleavage of only the selected target RNA within the entire human RNA pool. Only an unproductive binding but no cleavage occurs at other potential binding sites, since C^(16.1), X¹⁷, and elements S and Z₄ are required for cleavage. In addition, the disclosed compositions need not activate RNase H since they can be made with a low content of deoxyribonucleotides. This prevents induction of any unwanted non-specific cleavage.

[0058] Computer algorithms can be used to identify RNA substrates in sequence databases suitable for use with the disclosed compositions. An example of such an algorithm is (using the numbering according to FIG. 2):

[0059] i: find all C³ UGANGA(N)R sequences in a given mRNA;

[0060] ii: identify N^(2.1) and find potential N^(1.1)-N^(2.1) base pairs (in which N^(1.1) must be part of an N^(16.2)-C^(16.1)-N¹⁷-N^(1.1) sequence) in a region positioned approximately 30 nucleotides from C³ in the 3′ direction;

[0061] iii: calculate stem stabilities for stems which terminate at the above-mentioned N^(1.1)-N^(2.1) base pairs;

[0062] iv: sort according to stem stability.

[0063] A program based on these algorithms enables a very efficient search in databases or individual sequences. As a result, in addition to a suitable RNA target sequence, one obtains the sequence of the oligomer which is necessary to induce cleavage of this target sequence. In this connection it is important to also take into consideration potential target sites containing incomplete base pairs in the region of the stem structure (that is, element S) since several incomplete base pairs (mismatches) can be tolerated in this section.

[0064] Preferred RNA substrates for cleavage using the disclosed compositions are human cellular transcripts and transcripts of human or animal viruses as well as transcripts of bacteria and fungi that infect humans. Preferred RNA substrates are human dopamine D2 receptor mRNA, human brain cholecystokinin receptor mRNA, human serotonin 5-HT3 receptor mRNA, human alpha-2-macroglobulin receptor RNA, human tyrosine kinase-type receptor (HER2) mRNA, human interleukin 2 receptor beta chain mRNA, human MAD-3 mRNA, human bcl-1 mRNA, human bcl-2 mRNA, human cyclin F mRNA, human cyclin G1 mRNA, human bleomycin hydrolase mRNA, human acute myeloid leukemia 1 oncogene mRNA, human polycystic kidney disease 1 protein (PKD1) mRNA, transcripts of the bovine viral diarrhea virus, transcripts of the foot and mouth disease virus 3D gene and transcripts of the Epstein-Barr virus.

[0065] Particularly preferred cleavage motifs are located at the following positions of the RNA substrates (the name of the respective sequence in the EMBL Nucleotide Sequence Database 49th or 50th Edition is given in parentheses):

[0066] human dopamine D2 receptor mRNA (HSDRD2A) with N^(16.2) at position 2355 and a cleavage after the triplet UCU;

[0067] human brain cholecystokinin receptor mRNA (HSBRACHE) with N^(16.2) at position 1519 and a cleavage after the triplet ACA;

[0068] human serotonin 5-HT3 receptor mRNA (HSSSHT3RA) with N^(16.2) at position 467 and a cleavage after the triplet ACA;

[0069] human alpha-2-macroglobulin receptor RNA (HS2MRLR08) with N^(16.2) at position 776 and a cleavage after the triplet GCC;

[0070] human tyrosine kinase-type receptor (HER2) mRNA (HSHER2A) with N^(16.2) at position 3330 and a cleavage after the triplet ACU;

[0071] human interleukin 2 receptor beta chain mRNA (HSIL2RBC) with N^(16.2) at position 937 and a cleavage after the triplet ACA;

[0072] human MAD-3 mRNA (HSMAD3A) with N^(16.2) at position 138 and a cleavage after the triplet GCC;

[0073] human bcl-1 mRNA (HSBCL1G) with N^(16.2) at position 777 and a cleavage after the triplet GCA;

[0074] human bcl-2 mRNA (HSBCL2A) with N^(16.2) at position 4152 and a cleavage after the triplet ACC;

[0075] human cyclin F mRNA (HSCYCLF) with N^(16.1) at position 378 and a cleavage after the triplet ACA;

[0076] human cyclin G1 mRNA (HSCYCGIR) with N^(16.2) at position 166 and a cleavage after the triplet GCC;

[0077] human bleomycin hydrolase mRNA (HSBLEO) with N^(16.2) at position 1352 and a cleavage after the triplet ACA;

[0078] human acute myeloid leukemia 1 oncogene mRNA (HSAML1) with N^(16.2) at position 883 and a cleavage after the triplet GCC;

[0079] human polycystic kidney disease 1 protein mRNA (HSPKD1A) with N^(16.2) at position 11354 and a cleavage after the triplet GCC;

[0080] transcripts of the bovine viral diarrhea virus (BV25053) with N^(16.2) at position 616 and cleavage after the triplet GCC;

[0081] transcripts of the foot and mouth disease virus 3D gene (FMDV3D) with N^(16.2) at position 1291 and a cleavage after the triplet GCA; and

[0082] transcripts of the Epstein-Barr virus (HEEBVT2R) with N^(16.2) at position 1647 and a cleavage after the triplet GCA.

[0083] Flanking elements Z₁ and Z3 preferably contain, independently of each other, from 3 to 40, and more preferably from 5 to 10, nucleotides or nucleotide analogues. It is preferred that Z₁ and Z₁′ interact to form a stem of at least three base pairs, and that Z₃′ and Z₃′ interact to form a stem of at least three base pairs. It is more preferred that these stems are adjacent to Z₂. It is most preferable that Z₁ and Z₁′ interact to form a stem of more than three base pairs, and that Z₃ and Z₃′interact to form a stem of more than three base pairs.

Catalytic Core

[0084] Elements Z₂ and Z₄ are considered to form the catalytic core of the combination of a disclosed composition and an RNA substrate (see FIG. 2). Z₂ is preferably made up of nucleotide analogues. In element Z₂ it is preferred that each W (in structure (I)) is C₁-C₅ straight chain or branched alkyl, C₂-C₅ straight chain or branched alkenyl, C₂-C₅ straight chain or branched alkynyl, C₁-C₅ straight chain or branched alkoxy, C₂-C₅ straight chain or branched alkenyloxy, and C₂-C₅ straight chain or branched C₂-C₅ alkynyloxy. It is also preferred that in X^ ¹², W is NH₂, OH-substituted C₁-C₄ alkyl, OH-substituted C₂-C₄ alkenyl, OH-substituted C₁-C₄ alkoxy or OH-substituted C2-C₄ alkenyloxy. It is more preferred that in X^ ¹², W is NH₂, methoxy, 2-hydroxyethoxy, allyloxy or allyl. It is also preferred that in X¹², W is —H or —OH. It is also preferred that in each X¹³ and X¹⁴, W is C₁-C₄ alkyl, C₂-C₄ alkenyl, C₁-C₄ alkoxy, C₂-C₄ alkenyloxy, OH-substituted C₁-C₄ alkyl, OH-substituted C₂-C₄ alkenyl, OH-substituted C₁-C₄ alkoxy, or OH-substituted C₂-C₄ alkenyloxy. It is more preferred that in each X¹³ and X¹⁴, W is methoxy, 2-hydroxyethoxy or allyloxy.

[0085] The subunits in element Z₂ are preferably nucleotide analogues which can only hybridize weakly with ribonucleotides. Examples of such subunits are nucleotide analogues that contain a substituted or unsubstituted alkyl, alkenyl, alkynyl, alkoxy, alkenyloxy or alkynyloxy group, with preferably 1 to 5 carbon atoms, at the 2′ position of ribose. Preferred nucleobases which can be used in element Z₂ for this purpose are adenin-9-yl, purin-9-yl, guanin-9-yl and hypoxanthin-9-yl.

[0086] The following nucleotides and nucleotide analogues are preferred for element Z₂ (referring to components of structure (I)):

[0087] Position X¹²: B=guanin-9-yl, V=O, W=H; B=7deazaguanin-9-yl, V=O, W=OH; or B=guanin-9-yl, V=O, W=OH;

[0088] Position X¹³: B=adenin-9-yl, V=O, W=allyloxy; or B=adenin-9-yl, V=O, W=2-hydroxyethoxy; B=purin-9-yl, V=O, W=allyloxy;

[0089] Position X¹⁴: B=adenin-9-yl, V=O, W=allyloxy; B=purin-9-yl, V=O, W=OH; or B=adenin-9-yl, V=O, W=2-hydroxyethoxy; B=purin-9-yl, V=O, W=allyloxy;

[0090] Position X^(15.1): B=hypoxanthin-9-yl or a functional equivalent thereof, V=O, W=OH.

[0091] Elements Z₂ and Z₄ interact in a way that allows for the formation of a catalytic structure. In preferred compositions Z₂ and Z₄ interact in a way that allows for the formation of a catalytic structure resembling a hammerhead catalytic structure. One way Z₂ and Z₄ can interact to form a catalytic structure is through the interaction of the nucleotides and/or nucleotide analogues making up Z₂ and the nucleotides making up Z₄. The disclosed compositions are able to induce cleavage of an RNA substrate independent of RNase H. That is, the disclosed compositions are able to induce cleavage of an RNA substrate without involving RNase H. Although the disclosed compositions may also be capable of promoting cleavage of RNA by RNase H, it is preferred that they do not.

[0092] The 3′ end of the disclosed compositions can be protected against degradation by exonucleases by, for example, using a nucleotide analogue that is modified at the 3′ position of the ribose sugar (for example, by including a substituted or unsubstituted alkyl, alkoxy, alkenyl, alkenyloxy, alkynyl or alkynyloxy group as defined above). The disclosed compositions can also be stabilized against degradation at the 3′ end by exonucleases by including a 3′-3′-linked dinucleotide structure (Ortigao et al., Antisense Research and Development 2:129-146 (1992)) and/or two modified phospho bonds, such as two phosphorothioate bonds.

[0093] The disclosed compositions can also be linked to a prosthetic group in order to improve their cellular uptake and/or to enable a specific cellular localization. Examples of such prosthetic groups are polyamino acids (for example, polylysine), lipids, hormones or peptides. These prosthetic groups are usually linked via the 3′ or 5′ end of the oligomer either directly or by means of suitable linkers (for example, linkers based on 6-aminohexanol or 6-mercaptohexanol). These linkers are commercially available and techniques suitable for linking prosthetic groups to the oligomer are known to a person skilled in the art.

[0094] Increasing the rate of hybridization can be important for the biological activity of the disclosed compositions since in this way it is possible to achieve a higher activity at low concentrations of the composition. This is important for short-lived RNA substrates or RNA substrates that occur less often. A substantial acceleration of the hybridization can be achieved by, for example, coupling positively charged peptides (containing, for example, several lysine residues) to the end of an oligonucleotide (Corey J. Am. Chem. Soc. 117:9373-9374 (1995)). The disclosed compositions can be simply modified in this manner using the linkers described above. Alternatively, the rate of hybridization can also be increased by incorporation of subunits which contain sperminyl residues (Schmid and Behr, Tetrahedron Lett. 36:1447-1450 (1995)). Such modifications of the disclosed compositions also improve the ability to bind to RNA substrates having secondary structures.

Synthesis of Oligomers

[0095] The disclosed compositions can be synthesized using any suitable method. Many synthesis methods are known. The following techniques are preferred for synthesis of the disclosed compositions. 2′-O-Allyl modified oligomers that contain residual purine ribonucleotides, and bearing a suitable 3′-terminus such as an inverted thymidine residue (Ortigao et al., Antisense Research and Development 2:129-146 (1992)) or two phosphorothioate linkages at the 3′-terminus to prevent eventual degradation by 3′-exonucleases, can be synthesized by solid phase β-cyanoethyl phosphoramidite chemistry (Sinha et al., Nucleic Acids Res. 12:45394557 (1984)) on any commercially available DNA/RNA synthesizer. A preferred method is the 2′-O-tert-butyldimethylsilyl (TBDMS) protection strategy for the ribonucleotides (Usman et al., J. Am. Chem. Soc. 109:7845-7854 (1987)), and all the required 3′-O-phosphoramidites are commercially available. In addition, the use of aminomethylpolystyrene is preferred as the support material due to its advantageous properties (McCollum and Andrus Tetrahedron Letters 32:40694072 (1991)). Fluorescein can be added to the 5′-end of a substrate RNA during the synthesis by using commercially available fluorescein phosphoramidites. In general, a desired oligomer can be synthesized using a standard RNA cycle. Upon completion of the assembly, all base labile protecting groups are removed by an 8 hour treatment at 55° C. with concentrated aqueous ammonia/ethanol (3:1 v/v) in a sealed vial. The ethanol suppresses premature removal of the 2′-O-TBDMS groups which would otherwise lead to appreciable strand cleavage at the resulting ribonucleotide positions under the basic conditions of the deprotection (Usman et al., J. Am. Chem. Soc. 109:7845-7854 (1987)). After lyophilization the TBDMS protected oligomer is treated with a mixture of triethylamine trihydrofluoride/triethylamine/N-methylpyrrolidinone for 2 hours at 60° C. to afford fast and efficient removal of the silyl protecting groups under neutral conditions (Wincott et al., Nucleic Acids Res. 23:2677-2684 (1995)). The fully deprotected oligomer can then be precipitated with butanol according to the procedure of Cathala and Brunel (Nucleic Acids Res. 18:201 (1990)). Purification can be performed either by denaturing polyacrylamide gel electrophoresis or by a combination of ion-exchange HPLC (Sproat et al., Nucleosides and Nucleotides 14:255-273 (1995)) and reversed phase HPLC. For use in cells, it is preferred that synthesized oligomers be converted to their sodium salts by precipitation with sodium perchlorate in acetone. Traces of residual salts are then preferably removed using small disposable gel filtration columns that are commercially available. As a final step it is preferred that the authenticity of the isolated oligomers is checked by matrix assisted laser desorption mass spectrometry (Pieles et al., Nucleic Acids Res. 21:3191-3196 (1993)) and by nucleoside base composition analysis. In addition, a functional cleavage test with the oligomer and the corresponding chemically synthesized short oligoribonucleotide substrate is also preferred.

Cleavage of RNA Substrates

[0096] The disclosed compositions can have a very high in vivo activity since the RNA cleavage will be promoted by protein factors that are present in the nucleus or cytoplasm of the cell. Examples of such protein factors (which can increase the activity of hammerhead ribozymes) are, for example, the nucleocapsid protein NCp7 of HIVI (Muller et al., J. Mol. Biol. 242:422-429 (1994)) and the heterogeneous nuclear ribonucleoprotein Al (Heidenreich et al., Nucleic Acids Res. 23:2223-2228 (1995)). Thus, cleavage of long RNA transcripts can be efficiently induced within the cell by the disclosed compositions.

[0097] The disclosed compositions can be used in pharmaceutical compositions that contain one or several oligomers as the active substance, and, optionally, pharmaceutically acceptable auxiliary substances, additives and carriers. Such pharmaceutical compositions are suitable for the production of an agent to specifically inactivate the expression of genes in eukaryotes, prokaryotes and viruses, especially of human genes such as tumor genes or viral genes or RNA molecules in a cell. Further areas of application are the inactivation of the expression of plant genes or insect genes. Thus, the disclosed compositions can be used as drugs for humans and animals as well as a pesticide for plants.

[0098] A variety of methods are available for delivering the disclosed compositions to cells. For example, in general, the disclosed compositions can be incorporated within or on microparticles. As used herein, microparticles include liposomes, virosomes, microspheres and microcapsules formed of synthetic and/or natural polymers. Methods for making microcapsules and microspheres are known to those skilled in the art and include solvent evaporation, solvent casting, spray drying and solvent extension. Examples of useful polymers which can be incorporated into various microparticles include polysaccharides, polyanhydrides, polyorthoesters, polyhydroxides and proteins and peptides.

[0099] Liposomes can be produced by standard methods such as those reported by Kim et al., Biochim. Biophys. Acta, 728:339-348 (1983); Liu et al., Biochim. Biophys. Acta, 1104:95-101 (1992); and Lee et al., Biochim. Biophys. Acta., 1103:185-197 (1992); Wang et al., Biochem., 28:9508-9514 (1989)). Such methods have been used to deliver nucleic acid molecules to the nucleus and cytoplasm of cells of the MOLT-3 leukemia cell line (Thierry and Dritschilo, Nucl. Acids Res., 20:5691-5698 (1992)). Alternatively, the disclosed compositions can be incorporated within microparticles, or bound to the outside of the microparticles, either ionically or covalently.

[0100] Cationic liposomes or microcapsules are microparticles that are particularly useful for delivering negatively charged compounds such as the disclosed compounds, which can bind ionically to the positively charged outer surface of these liposomes. Various cationic liposomes have previously been shown to be very effective at delivering nucleic acids or nucleic acid-protein complexes to cells both in vitro and in vivo, as reported by Felgner et al., Proc. Natl. Acad. Sci. USA, 84:7413-7417 (1987); Felgner, Advanced Drug Delivery Reviews, 5:163-187 (1990); Clarenc et al., Anti-Cancer Drug Design, 8:81-94 (1993). Cationic liposomes or microcapsules can be prepared using mixtures including one or more lipids containing a cationic side group in a sufficient quantity such that the liposomes or microcapsules formed from the mixture possess a net positive charge which will ionically bind negatively charged compounds. Examples of positively charged lipids that may be used to produce cationic liposomes include the aminolipid dioleoyl phosphatidyl ethanolamine (PE), which possesses a positively charged primary amino head group; phosphatidylcholine (PC), which possess positively charged head groups that are not primary amines; and N[1-(2,3-dioleyloxy)propyl]-N,N,N-triethylammonium (“DOTMA,” see Felgner et al., Proc. Natl. Acad. Sci USA, 84:7413-7417 (1987); Felgner et al., Nature, 337:387-388 (1989); Felgner, Advanced Drug Delivery Reviews, 5:163-187 (1990)).

[0101] A preferred form of microparticle for delivery of the disclosed compositions are heme-bearing microparticles. In these microparticles, heme is intercalated into or covalently conjugated to the outer surface of the microparticles. Heme-bearing microparticles offer an advantage in that since they are preferentially bound and taken up by cells that express the heme receptor, such as hepatocytes, the amount of drug required for an effective dose is significantly reduced. Such targeted delivery may also reduce systemic side effects that can arise from using relatively high drug concentrations in non-targeted delivery methods. Preferred lipids for forming heme-bearing microparticles are 1,2-dioleoyloxy-3-(trimethylammonium) propane (DOTAP) and dioleoyl phosphatidyl ethanolamine (DOPE). The production and use of heme-bearing microparticles are described in PCT application WO 95/27480 by Innovir.

[0102] The disclosed compositions can also be encapsulated by or coated on cationic liposomes which can be injected intravenously into a mammal. This system has been used to introduce DNA into the cells of multiple tissues of adult mice, including endothelium and bone marrow, where hematopoietic cells reside (see, for example, Zhu et al., Science, 261:209-211 (1993)).

[0103] Liposomes containing the disclosed compositions can be administered systemically, for example, by intravenous or intraperitoneal administration, in an amount effective for delivery of the disclosed compositions to targeted cells. Other possible routes include trans-dermal or oral, when used in conjunction with appropriate microparticles. Generally, the total amount of the liposome-associated oligomer administered to an individual will be less than the amount of the unassociated oligomer that must be administered for the same desired or intended effect.

[0104] Compositions including various polymers such as the polylactic acid and polyglycolic acid copolymers, polyethylene, and polyorthoesters and the disclosed compositions can be delivered locally to the appropriate cells by using a catheter or syringe. Other means of delivering such compositions locally to cells include using infusion pumps (for example, from Alza Corporation, Palo Alto, Calif. or incorporating the compositions into polymeric implants (see, for example, Johnson and Lloyd-Jones, eds., Drug Delivery Systems (Chichester, England: Ellis Horwood Ltd., 1987), which can effect a sustained release of the therapeutic compositions to the immediate area of the implant.

[0105] For therapeutic applications the active substance is preferably administered at a concentration of 0.01 to 10,000 μg/kg body weight, more preferably of 0.1 to 1000 μg/kg body weight. The administration can, for example, be carried out by injection, inhalation (for example as an aerosol), as a spray, orally (for example as tablets, capsules, coated tablets etc.), topically or rectally (for example as suppositories).

[0106] The disclosed compositions can be used in a method for the specific inactivation of the expression of genes in which an active concentration of the composition is taken up into a cell so that the composition induces specific cleavage of a predetermined RNA molecule which is present in the cell, the cleavage preferably occurring catalytically. Similar compositions, which are described in U.S. Pat. No. 5,334,711, have been used successfully in mice to inactivate a gene (Lyngstadaas et al., EMBO J. 14:5224-5229 (1995)). This process can be carried out in vitro on cell cultures as well as in vivo on living organisms (prokaryotes or eukaryotes such as humans, animals or plants).

[0107] The disclosed compositions can also be used as RNA restriction enzymes to induce cleavage of RNA molecules (in, for example, cell free in vitro reactions). The disclosed compositions can also be used in a reagent kit for the restriction cleavage of RNA molecules which contains, for example, an oligomer and suitable buffer substances. In this case the oligomer and the buffer substances can be present in the form of solutions, suspensions or solids such as powders or lyophilisates. The reagents can be present together, separated from one another or optionally also on a suitable carrier. The disclosed compositions can also be used as a diagnostic agent or to identify the function of unknown genes.

[0108] The present invention will be further understood by reference to the following non-limiting examples.

Examples

[0109] The following examples demonstrate that compositions having motifs forming structures resembling hammerheads but which include I^(15.1) and C^(16.1) can result in specific cleavage of an RNA molecule. Although the examples involve the use of oligomers having RNA cleaving activity and including motifs corresponding to both elements Z₂ and Z₄ (the oligomers in the examples are thus analogous to a Gerlach type ribozyme), the activities are indicative of the cleavage inducing activity of the disclosed compositions.

Example 1 Cleavage Reactions which Indicate that an Inosine Substitution at Position 15.1 can Effectively Cleave N^(16.2)C^(16.1)H¹⁷

[0110] A set of 12 substrates was synthesized which covered each permutation of the N^(16.2)C^(16.1)H¹⁷ motif where H¹⁷ is not guanosine. The oligomers and the corresponding substrates used in the cleavage assays are shown in Table 1. Each of the substrates was labeled with fluorescein at the 5′ end and an inverted thymidine cap was used on the 3′-end. A set of four catalytic oligomers was synthesized, providing an appropriately matched catalytic oligomer for each of the substrates. Each of these catalytic oligomers had an inosine at position 15.1. The catalytic oligomers were similar to those described in U.S. Pat. No. 5,334,711 except for the substitution of I for A at position 15.1. The catalytic oligomers includes, in a single molecule, the equivalent of elements Z₄, Z₁′, Z₁, Z₂ and Z₃ in the compositions and RNA substrates as described above. A control substrate and catalytic oligomer were also synthesized in which there was a U at position 16.1 of the substrate and an A at position 15.1 of the catalytic oligomer. TABLE 1 N^(16.2)N^(16.1)H₁₇ Triplet Substrate sequence ACC Fl-GAAUACCGGUCGC*T (SEQ ID NO: 4) ACA Fl-GAAUACAGGUCGC*T (SEQ ID NO: 5) ACU Fl-GAAUACUGGUCGC*T (SEQ ID NO: 6) GCC Fl-GAAUACAGGUCGC*T (SEQ ID NO: 7) GCA Fl-GAAUGCAGGUCGC*T (SEQ ID NO: 8) GCU Fl-GAAUGCUGGUCGC*T (SEQ ID NO: 9) CCC Fl-GAAUCCCGGUCGC*T (SEQ ID NO: 1O) CCA Fl-GAAUCCAGGUCGC*T (SEQ ID NO: 11) CCU Fl-GAAUCCUGGUCGC*T (SEQ ID NO: 12) UCC Fl-GAAUUCCGGUCGC*T (SEQ ID NO: 13) UCA Fl-GAAUUCAGGUCGC*T (SEQ ID NO: 14) UCU Fl-GAAUUCUGGUCGC*T (SEQ ID NO: 15) GUC Fl-GAAUGUCGGUCGC*T (SEQ ID NO: 16) Targeted Catalytic triplet oligomer sequence ACH gcgacccuGAuGaggccgug (SEQ ID NO: 17) aggccGaaIuauuc*T GCH gcgacccuGAuGaggccgug (SEQ ID NO: 18) aggccGaaIcauuc*T CCH gcgacccuGAuGaggccgug (SEQ ID NO: 19) aggccGaaIgauuc*T UCH gcgacccuGAuGaggccgug (SEQ ID NO: 20) aggccGaaIaauuc*T GUC gcgacccuGAuGaggccgug (SEQ ID NO: 21) aggccGaaAcauuc*T

[0111] The above substrates and catalytic oligomers were used in cleavage reactions to determine the ability of an inosine at position 15.1 to overcome the requirement of a U at position 16.1 for cleavage. All of the reactions were performed using the following protocol. The reactions were typically done in 100 μl and they contained distilled, autoclaved H₂O, 10 mM MgCl₂, 10 mM Tris-HCl pH 7.4, 5 μM ribozyme, and 0.25 μM substrate. The catalytic oligomer, substrate, and buffer were added together and heated to 95° C. for 5 minutes. After cooling to room temperature over 5 minutes the reactions were brought to 10 mM MgCl₂, mixed, and placed at 37° C. 10 μL aliquots were removed at specific time intervals (10, 30, 60, and 120 minutes) and added to 3 μl of loading buffer (95% formamide, 100 mM EDTA pH 8.0, 0.05% bromophenol blue) to quench the reaction. Samples were analyzed by 20% polyacrylamide gel electrophoresis. Gels were analyzed on a Molecular Dynamics Fluorescence Imager. The results of cleavage reactions of this type, using the substrates and catalytic oligomers shown in Table 1, are shown in Table 2. TABLE 2 N^(16.2) N^(16.1) H¹⁷ After Triplet mixing 10 30 60 120 I^(15.1) U^(15.2) Catalytic oligomer ACC 4.4 28.2 58.1 91.5 91.5 ACA 7.7 71.8 84.7 93.1 94.8 ACU 1.8 58.7 70.5 I^(15.1) C^(15.2) Catalytic oligomer GCC 1.62 39.6 59.9 82.0 87.0 GCA 13.7 65.3 78.7 89.7 93.1 GCU — 64.3 74.8 I^(15.1) G^(15.2) Catalytic oligomer CCC — 34.33 45.38 CCA 1.1 18.8 45.5 70.8 80.63 CCU 2.0 28.4 36.7 I^(15.1) A^(15.2) Catalytic oligomer UCC 6.8 57.0 64.7 UCA 1.6 39.6 60.8 UCU 3.3 41.1 53.1 A^(15.1) C^(15.2) Catalytic oligomer GUC 1.6 38.5 66.5 93.5

[0112] The numbers represent the percentage of substrate cleaved at the indicated time point (which were at 0, 10, 30, 60, and 120 minutes after starting the reaction). The results indicate that substrates with a C at position 16.1 are able to be cleaved by catalytic oligomers containing an I at position 15.1. While there are differences between the various substrates at the 120 minute time point, the data show that a substrate with a C at position 16.1 in conjunction with a catalytic oligomer with an I at position 15.1 is able to effectively cleave in all backgrounds, indicating that the substitution of an I at position 15.1 does in fact allow for the cleavage of any appropriate substrate containing a N^(16.2)C^(16.1)H¹⁷ site.

[0113] Initial rates of cleavage of the twelve substrates having C^(16.1), and the control substrate having U^(16.1), by the corresponding catalytic oligomers (all shown in Table 1) were determined using single turnover kinetics. Single turnover kinetics were assessed by mixing 2.5 μl of a 100 μM ribozyme solution, 2.5 μl of a 10 μM solution of 5′ fluorescein labeled substrate, and 10 μl of a 100 mM Tris-HCl pH 7.4 solution. The mixture was diluted to a final volume of 90 μl, heated to 95° C. for 5 minutes, and cooled to 37° C. The reaction was started by adding 10 μl of a 100 mM MgCl₂ solution. The final concentrations of the reaction components were 250 nM substrate, 2.5 μmol ribozyme, and 10 mM MgCl₂. Ten microliter samples were removed at various times and mixed with 10 μl of a 100 mM EDTA, bromphenol blue solution to stop the reaction. Cleavage products were separated from unreacted substrate by PAGE and were quantitated on a Molecular-Dynamics Fluorescence Imager.

[0114] The data, measured in fraction of substrate cleaved versus time, were fitted to the equation:

frac[P]=H ₀(1-e ^(−k) ^(₂) ^(t))/S₀

[0115] as described by Jankowsky and Schwenzer, Nucl. Acids Res. 24:433 (1996). The calculated values of k₂ for the various ribozymes are shown in Table 3. TABLE 3 N^(16.2)N^(16.1)H¹⁷ Triplet k₂ (min⁻¹) Substrate sequence gcgacccuGAuGaggccgugaggccGaaIuauuc*T (SEQ ID NO: 17) ACC 0.07 Fl-GAAUACCGGUCGC*T (SEQ ID NO: 4) ACA 0.36 Fl-GAAUACAGGUCGC*T (SEQ ID NO: 5) ACU 0.026 Fl-GAAUACUGGUCGC*T (SEQ ID NO: 6) gcgacccuGAuGaggccgugaggccGaaIcauuc*T (SEQ ID NO: 18) GCC 0.12 Fl-GAAUGCCGGUCGC*T (SEQ ID NO: 7) GCA 0.48 Fl-GAAUGCAGGUCGC*T (SEQ ID NO: 8) GCU 0.05 Fl-GAAUGCUGGUCGC*T (SEQ ID NO: 9) gcgacccuGAuGaggccgugaggccGaaIgauuc*T (SEQ ID NO: 19) CCC <0.01 Fl-GAAUCCCGGUCGC*T (SEQ ID NO: 10) CCA 0.04 Fl-GAAUCCAGGUCGC*T (SEQ ID NO: 11) CCU <0.01 Fl-GAAUCCUGGUCGC*T (SEQ ID NO: 12) gcgacccuGAuGaggccgugaggccGaaIaauuc*T (SEQ ID NO: 20) UCC <0.01 Fl-GAAUUCCGGUCGC*T (SEQ ID NO: 13) UCA <0.01 Fl-GAAUUCAGGUCGC*T (SEQ ID NO: 14) UCU <0.01 Fl-GAAUUCUGGUCGC*T (SEQ ID NO: 15) gcgacccuGAuGaggccgugaggccGaaAcauuc*T (SEQ ID NO: 21) GUC 0.13 Fl-GAAUGUCGGUCGC*T (SEQ ID NO: 16)

[0116] The results show that substrates with A^(16.2)C^(16.1)H¹⁷ and G^(16.2)C^(16.1)H¹⁷ triplets are cleaved at a high rate. Comparison to the control catalytic oligomer having an A at position 15.1 (to cleave a substrate with a G^(16.2)U^(16.1)C¹⁷ triplet) shows that substrates with A^(16.2)C^(16.1)A¹⁷ and G^(16.2)C^(16.1)A¹⁷ triplets (to be cleaved by a catalytic oligomer with an I at position 15.1) have an initial rate of cleavage that is higher than the corresponding control reactions involving reactants with a standard A^(15.1)-U^(16.1) base pair.

[0117] Publications cited herein and the material for which they are cited are specifically incorporated by reference.

[0118] Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. Such equivalents are intended to be encompassed by the following claims.

1 21 1 57 RNA Artificial Sequence Description of Artificial Sequence Hammerhead ribozyme 1 nnnnnnnnnn nnnnnncuga nganrnnnnn nnnnnnnyng aarnnnnnnn nnnnnuh 57 2 14 RNA Artificial Sequence Description of Artificial Sequence oligomer that induces cleavage of the RNA substrate 2 nnnnyngaan nnnn 14 3 35 RNA Artificial Sequence Description of Artificial Sequence RNA substrate 3 nnnnchnnnn nnnnnnnnnn nncugangan rnnnn 35 4 14 RNA Artificial Sequence Description of Artificial Sequence oligonucleotide substrate 4 gaauaccggu cgcn 14 5 14 RNA Artificial Sequence Description of Artificial Sequence oligonucleotide substrate 5 gaauacaggu cgcn 14 6 14 RNA Artificial Sequence Description of Artificial Sequence oligonucleotide substrate 6 gaauacuggu cgcn 14 7 14 RNA Artificial Sequence Description of Artificial Sequence oligonucleotide substrate 7 gaaugccggu cgcn 14 8 14 RNA Artificial Sequence Description of Artificial Sequence oligonucleotide substrate 8 gaaugcaggu cgcn 14 9 14 RNA Artificial Sequence Description of Artificial Sequence oligonucleotide substrate 9 gaaugcuggu cgcn 14 10 14 RNA Artificial Sequence Description of Artificial Sequence oligonucleotide substrate 10 gaaucccggu cgcn 14 11 14 RNA Artificial Sequence Description of Artificial Sequence oligonucleotide substrate 11 gaauccaggu cgcn 14 12 14 RNA Artificial Sequence Description of Artificial Sequence oligonucleotide substrate 12 gaauccuggu cgcn 14 13 14 RNA Artificial Sequence Description of Artificial Sequence oligonucleotide substrate 13 gaauuccggu cgcn 14 14 14 RNA Artificial Sequence Description of Artificial Sequence oligonucleotide substrate 14 gaauucaggu cgcn 14 15 14 RNA Artificial Sequence Description of Artificial Sequence oligonucleotide substrate 15 gaauucuggu cgcn 14 16 14 RNA Artificial Sequence Description of Artificial Sequence oligonucleotide substrate 16 gaaugucggu cgcn 14 17 35 RNA Artificial Sequence Description of Artificial Sequence Catalytic Oligomer 17 gcgacccuga ugaggccgug aggccgaanu auucn 35 18 35 RNA Artificial Sequence Description of Artificial Sequence Catalytic Oligomer 18 gcgacccuga ugaggccgug aggccgaanc auucn 35 19 35 RNA Artificial Sequence Description of Artificial Sequence Catalytic Oligomer 19 gcgacccuga ugaggccgug aggccgaang auucn 35 20 35 RNA Artificial Sequence Description of Artificial Sequence Catalytic Oligomer 20 gcgacccuga ugaggccgug aggccgaana auucn 35 21 35 RNA Artificial Sequence Description of Artificial Sequence Catalytic Oligomer 21 gcgacccuga ugaggccgug aggccgaaac auucn 35 

We claim:
 1. A composition that induces cleavage of an RNA substrate, the composition comprising: 5′-Z₁-Z₂-Z₃-3′wherein Z₁ and Z₃ are oligomeric sequences which (1) are comprised of nucleotides, nucleotide analogues, or both, or (2) are oligonuleotide analogues, wherein the oligomeric sequences specifically interact with the RNA substrate by hybridization. wherein Z₂ consists of 5′-X¹²X¹³X¹⁴X^(15.1)-3′, or5′-X¹²X¹³X¹⁴X^(15.1)-3′, wherein Z₂ is comprised of nucleotides, nucleotide analogues, or both, wherein the nucleotides and nucleotide analogues each have the structure

wherein each B is independently adenin-9-yl, cytosin-1-yl, guanin-9-yl, uracil-1-yl, uracil-5-yl, hypoxanthin-9-yl, thymin-1-yl, 5-methylcytosin-1-yl, 2,6-diaminopurin-9-yl, purin-9-yl, 7-deazaadenin-9-yl, 7-deazaguanin-9-yl, 5-propynylcytosin-1-yl, 5-propynyluracil-1-yl, isoguanin-9-yl, 2-aminopurin-9-yl, 6-methyluracil-1-yl, 4-thiouracil-1-yl, 2-pyrimidone-1-yl, quinazoline-2,4-dione-1-yl, xanthin-9-yl, N²-dimethylguanin-9yl or a functional equivalent thereof, wherein each V is independently an O, S, NH, or CH₂ group, wherein each W is independently selected from the group consisting of —H, —OH, —COOH, —CONH₂, —CONHR¹, —CONR¹R², —NH₂, —NHR¹, —NR¹R², —NHCOR¹, —SH, SR¹, —F, —ONH₂, —ONHR¹, —ONR¹R², —NHOH, —NHOR¹, —NR²OH, —NR²OR¹, substituted or unsubstituted C₁-C₁₀ straight chain or branched alkyl, substituted or unsubstituted C₂-C₁₀ straight chain or branched alkenyl, substituted or unsubstituted C₂-C₁₀ straight chain or branched alkynyl, substituted or unsubstituted C₁-C₁₀ straight chain or branched alkoxy, substituted or unsubstituted C₂-C₁₀ straight chain or branched alkenyloxy, and substituted or unsubstituted C₂-C₁₀ straight chain or branched alkynyloxy, wherein the substituents are independently halogen, cyano, amino, carboxy, ester, ether, carboxamide, hydroxy, or mercapto, wherein R¹ and R² are, independently, substituted or unsubstituted alkyl, alkenyl, or alkynyl groups, where the substituents are independently halogen, cyano, amino, carboxy, ester, ether, carboxamide, hydroxy, or mercapto, wherein D and E are residues which together form a phosphodiester or phosphorothioate diester bond between adjacent nucleosides or nucleoside analogues or together form an analogue of an internucleosidic bond, wherein in X^(15.1), B is hypoxanthin-9-yl or a functional equivalent thereof, wherein in X¹², B is independently guanin-9-yl, hypoxanthin-9-yl or 7-deazaguanin-9-yl; wherein in X¹³ and X¹⁴, B is independently adenin-9-yl, 2,6-diaminopurin-9-yl, purin-9-yl or 7-deazaadenin-9-yl; wherein in X^ ¹², B is independently adenin-9-yl, cytosin-1-yl, guanin-9-yl, uracil-1-yl, uracil-5-yl, hypoxanthin-9-yl, thymin-1-yl, 5-methylcytosin-1-yl, 2,6-diaminopurin-9-yl, purin-9-yl, 7-deazaadenin-9-yl, 7-deazaguanin-9-yl, 5-propynylcytosin-1-yl, 5-propynyluracil-1-yl, isoguanin-9-yl, 2-aminopurin-9-yl, 6-methyluracil-1-yl, 4-thiouracil-1-yl, 2-pyrimidone-1-yl, quinazoline-2,4-dione-1-yl, xanthin-9-yl, N²-dimethylguanin-9-yl or a functional equivalent thereof.
 2. The composition of claim 1 wherein the RNA substrate comprises 5′-Z₃-C^(16.1)-X¹⁷-S-Z₄-Z₁′-3′,wherein Z₁′ and Z₃′ interact with Z₁ and Z₃, wherein C^(16.1) is cytidine, wherein X¹⁷ is adenosine, guanosine, cytidine, or uridine, wherein S comprises a sequence capable of forming a hairpin structure, wherein cleavage occurs 3′ of X¹⁷, wherein Z₄ consists of 5′-X³X⁴X⁵X⁶X⁷X⁸X⁹-3′, or5′-X³X⁴X⁵X⁶X⁷X⁸X⁹^ -3′ wherein X⁵ and X⁸ are guanosine, wherein X⁶ and X⁹ are adenosine, wherein X⁴ is uridine, wherein X³ is cytidine, and wherein X⁷ and X^(9^) are independently adenosine, guanosine, cytidine, or uridine.
 3. The composition of claim 2 wherein X¹⁷ is adenosine, cytidine, or uridine.
 4. The composition of claim 1, wherein Z₁ and Z₃ do not contain any pyrimidines that are ribonucleotides.
 5. The composition of claim 1, wherein Z₁ and Z₃ do not contain any ribonucleotides.
 6. The composition of claim 1, wherein Z₁ and Z3 are comprised of nucleotides, nucleotide analogues, or both, wherein the nucleotides and nucleotide analogues each have the structure

wherein each B is independently adenin-9-yl, cytosin-1-yl, guanin-9-yl, uracil-1-yl, uracil-5-yl, hypoxanthin-9-yl, thymin-1-yl, 5-methylcytosin-1-yl; 2,6-diaminopurin-9-yl, purin-9-yl, 7-deazaadenin-9-yl, 7-deazaguanin-9-yl, 5-propynylcytosin-1-yl, 5-propynyluracil-1-yl, isoguanin-9-yl, 2-aminopurin-9-yl, 6-methyluracil-1-yl, 4-thiouracil-1-yl, 2-pyrimidone-1-yl, quinazoline-2,4-dione-1-yl, xanthin-9-yl, N²-dimethylguanin-9-yl or a functional equivalent thereof, wherein each V is independently an 0, S, NH, or CH₂ group, wherein each W is independently selected from the group consisting of substituted or unsubstituted C₁-C₁₀ straight chain or branched alkyl, C₂-C₁₀ straight chain or branched alkenyl, C₂-C₁₀ straight chain or branched alkynyl, C₁-C₁₀ straight chain or branched alkoxy, C₂-C₁₀ straight chain or branched alkenyloxy, and C₂-C₁₀ straight chain or branched alkynyloxy, wherein D and E are residues which together form a phosphodiester or phosphorothioate diester bond between adjacent nucleosides or nucleoside analogues or together form an analogue of an internucleosidic bond.
 7. The composition of claim 1, wherein Z₁ and Z₃ each independently contain from 3 to 40 nucleotides, nucleotide analogues, or a combination.
 8. The composition of claim 1, wherein Z₂ contains one or several nucleotide analogues wherein each W is independently selected from the group consisting of C₁-C₅ straight chain or branched alkyl, C₂-C₅ straight chain or branched alkenyl, C₂-C₅ straight chain or branched alkynyl, C₁-C₅ straight chain or branched alkoxy, C₂-C₅ straight chain or branched alkenyloxy, and C₂-C₅ straight chain or branched C₂-C₅ alkynyloxy.
 9. The composition of claim 1, wherein the free 3′ end is protected against exonuclease degradation.
 10. The composition of claim 1, wherein in X^ ¹² W is independently NH₂, OH-substituted C₂-C₄ alkyl, OH-substituted C₂-C₄ alkenyl, OH-substituted C₁-C₄ alkoxy or OH-substituted C₂-C₄ alkenyloxy.
 11. The composition of claim 10, wherein in X^ ¹² W is independently NH₂, methoxy, 2-hydroxyethoxy, allyloxy or allyl.
 12. The composition of claim 1, wherein X¹² is a ribonucleotide.
 13. The composition of claim 1, wherein X¹³ and X¹⁴, or a combination is a nucleotide analogue in which each W is independently C₁-C₄ alkyl, C₂-C₄ alkenyl, C₁-C₄ alkoxy, C₂-C₄ alkenyloxy, OH-substituted C₁-C₄ alkyl, OH-substituted C₂-C₄ alkenyl, OH-substituted C₁-C₄ alkoxy, or OH-substituted C₂-C₄ alkenyloxy.
 14. The composition of claim 13, wherein X¹³ and X¹⁴, or a combination is a nucleotide analogue in which each W is independently methoxy, 2-hydroxyethoxy or allyloxy.
 15. The composition of claim 1, wherein the RNA substrate is selected from the group consisting of human dopamine D2 receptor mRNA, human brain cholecystokinin receptor mRNA, human serotonin 5-HT3 receptor mRNA, human alpha-2-macroglobulin receptor RNA, human tyrosine kinase-type receptor (HER2) mRNA, human interleukin 2 receptor beta chain mRNA, human MAD-3 mRNA, human bcl-1 mRNA, human bcl-2 mRNA, human cyclin F mRNA, human cyclin G1 mRNA, human bleomycin hydrolase mRNA, human acute myeloid leukemia 1 oncogene mRNA, human polycystic kidney disease 1 protein (PKD1) mRNA, transcripts of the bovine viral diarrhea virus, transcripts of the foot and mouth disease virus 3D gene and transcripts of the Epstein-Barr virus.
 16. The composition of claim 1, wherein X^(15.1) is a ribonucleotide.
 17. A method for the specific cleavage of an RNA substrate, the method comprising bringing into contact the composition of claim 1 and the RNA substrate.
 18. The method of claim 17, wherein the RNA substrate is selected from the group consisting of human dopamine D2 receptor mRNA, human brain cholecystokinin receptor mRNA, human serotonin 5-HT3 receptor mRNA, human alpha-2-macroglobulin receptor RNA, human tyrosine kinase-type receptor (HER2) mRNA, human interleukin 2 receptor beta chain mRNA, -human MAD-3 mRNA, human bcl-1 mRNA, human bcl-2 mRNA, human cyclin F mRNA, human cyclin G1 mRNA, human bleomycin hydrolase mRNA, human acute myeloid leukemia 1 oncogene mRNA, human polycystic kidney disease 1 protein (PKD1) mRNA, transcripts of the bovine viral diarrhea virus, transcripts of the foot and mouth disease virus 3D gene and transcripts of the Epstein-Barr virus.
 19. A method of identifying the function of a gene, the method comprising bringing into contact the composition of claim 1 and a cell containing the gene, wherein the composition reduces expression of the gene, and observing any change in the cell.
 20. A method of treating a disease that is associated with an RNA molecule, the method comprising administering to a subject having the disease the composition of claim 1, wherein the RNA substrate is the RNA molecule associated with the disease.
 21. The method of claim 20 wherein the RNA molecule is an RNA molecule that is overexpressed. 